Name:
BIOCHEMISTRY I (CHEM 360)
EXAM 3
November 23, 2016
There are six pages, TEN questions, and a total of 115 points in this exam,
which gives 15 extra points on top of that required for a “perfect” paper.
Please read each question carefully and possibly more than once. Good luck…
(6)
1.
Standard free energies of hydrolysis for a series of “high energy” metabolites are given in the table below.
On the basis of these values provide structures for the missing reactant and the product in the reaction.
(8)
2.
When 13C labeled oxaloacetate is incorporated into a castor bean plant, the labeled carbon ends up at the
aldehyde carbon of glyoxylate at the end of the glyoxylate cycle. Identify the labeled carbon in
oxaloacetate.
Assume full conversion at the step catalyzed by isocitrate lyase. Show your work.
(15)
3.
Complete the following reactions by showing the full structures of the missing products
Please do not use abbreviations.
3.1.
3.2.
3.2.1.
Identify the pathway
in which the reaction
in 3.2 is observed
Use curly arrows to
show brief details of
mechanism
Page 2
Question submitted by Alyssa
(21)
4.
A number of electron transfer reactions take place within the pyruvate dehydrogenase (PDH) complex
during the conversion of pyruvate into acetyl CoA.
The standard reduction potentials (Eo’ ) for two of these half reactions are given.
4.1.
Give two possible overall reactions (only one of which is likely to be spontaneous)
4.2.
What general thermodynamic parameter (other than E) is used as a criterion to determine which
overall reaction is spontaneous (explain)
4.3.
Calculate E for the spontaneous overall reaction (assume all species are at 1.0 M
concentration and in the presence of the PDH complex).
4.4.
Identify the electron donor and the electron acceptor in the spontaneous overall reaction.
4.5.
Write the key structural features of the oxidized species at the end of the spontaneous overall
reaction.
(12)
5.
Pyruvate dehydrogenase complex deficiency (PDCD) is a neurodegenerative disorder commonly observed
in children.
2.1.
The shortage of which common metabolite is caused due to PDCD?
2.2.
Which common metabolic pathway is severely slowed down due to PDCD?
2.3.
Elevated levels of which amino acid is a diagnostic lead for PDCD?
Page 3
(24)
6.
Circle the best correct answer (only ONE) for the multiple-choice questions below.
Question submitted by Hyo
6.1.
Which of the following amino acids can be a precursor to a Citric Acid Cycle metabolite?
(1) alanine
6.2.
(2) aspartate
(3) glutamate
(4) all of the amino acids listed here
Cholera toxins effect the adenylyl cyclase signaling pathway by preventing G
proteins from functioning properly. Which of the following can be attributed to
the malfunction?
(1) Underproduction of succinate dehydrogenase
(2) Overproduction of cyclic AMP
(3) Deactivation of hormone receptor
(4) Activation of GTPase activity
6.3.
Which of the following two pathways is not likely to occur together?
(1) glycolysis and Krebb’s cycle (2) glyoxylate pathway and gluconeogenesis
(3) gluconeogenesis and glycogen synthesis
(4) glycogenolysis and glycolysis
6.4.
Under fasting conditions almost all the glucose to the body is supplied by
(1) The citric acid cycle
(4) ATP
6.2.
(2) gluconeogenesis
(5) reverse osmosis
(3) glycolysis
Once inside the cell, glucose is rapidly phosphorylated to glucose-6-phosphate. What is the main
purpose of this phosphorylation?
(1) To keep glucose inside the cell
(3) To form a high-energy compound
(2) To prevent mutarotation
(4) To activate PFK-1
6.2.
Out of the following fatty acids which one has the lowest melting point?
6.4.
For the reaction below what is the most likely value for G?
ATP
+
2 ADP
AMP
Page 4
(1) 0 kJ/mole
6.5.
(2) 30 kJ/mole
(3) -30 kJ/mole (4) It cannot be predicted
Which class of membrane proteins can be removed from the membrane by changing the ionic
strength of the solution?
(1) integral
(4) all of the above
(2) peripheral
(3) fatty acid-anchored
6.6.
How many ATP molecules are produced in the triose stage of glycolysis for each molecule of
glucose?
(1) 1
(2) 2
(3) 3
(4) 4
(5) ATP is consumed, not produced.
6.8.
All but one of the compounds below is likely to undergo a C-C bond cleavage reaction in the
presence of an “aldolase like” enzyme. Which compound will not undergo such reaction?
Page 5
(10)
7.
A representation of the thioester intermediate formed (following oxidation) in the active site of
glyceraldehyde-3-phosphate dehydrogenase is shown below.
7.1.
Draw a representative structure of the intermediate formed if the active site contained serine
instead of cysteine (with the rest of the active site remaining unaltered)
7.2.
The next step of the reaction is an attack by an inorganic phosphate (linked to his). Show the next
step on the “more preferential” acyl intermediate (the one you have provided for 7.1 or the one
given above). Give the product formed.
7.3.
Explain your choice of “more preferential” acyl intermediate
Page 6
(6)
Hers’ disease, considered as a glycogen storage disorder, is caused by a defective enzyme: liver
phosphorylase. Predict the effect of Hers’ disease on blood glucose levels. Substantiate your prediction(s).
8.
(6)
9.
Tyrosine Kinase is an integral protein and an insulin receptor. The signaling actions of insulin are mediated
through PIP2 via insulin receptor substrate (IRS) proteins. However, in contrast to the
inositol-phospholipid signaling pathway, PIP 2 is not effected by phosphor lipase (PLC) but undergoes s
reaction catalyzed by a kinase forming a different second messenger.
Identify the “different” second messenger described above.
You will get points by writing the acronym for the second messenger; but you will need to provide a
structure with key features for full credit.
Question submitted by Milton
(9)
10.
How many oxidation steps are there in glycolysis?
In the absence of oxygen the muscle cells are able to regenerate an oxidizing agent to supplement the
“needs” of glycolysis. Write the relevant reaction starting from a glycolysis metabolite. Show all the
coenzymes involved.
1.
In the absence of oxygen, muscle cells are able to convert pyruvate into lactate, and thus convert NADH
back to NAD+. Explain the purpose of renewing NAD+. (Why not just use NADH to make ATP?!)
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105
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